American Society for MicrobiologyThe American Society for Microbiology (ASM) is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators.http://www.asm.org
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ASM understands the vital importance clinical microbiology plays in sustaining the health of the world population. We know the daily challenges that you face in the prevention, diagnosis, and treatment of infectious disease. ASM supports the clinical microbiological community in many unique ways – with cutting-edge information, professional certification and awards, and a robust advocacy for the field. Here is how we can help you…

Access to cutting-edge information through:

ASM’s Microbe 2017 meeting, combining the dedicated clinical track of the former General Meeting with the premier infectious disease offerings of ICAAC

Awards and recognition specifi cally focused on clinical microbiologists including the BD Award for Research in Clinical Microbiology, Scherago-Rubin Award, and the Beckman-Coulter Young Investigator Award

ASM understands the vital importance clinical microbiology plays in sustaining the health of theworld population. We know the daily challenges that you face in the prevention, diagnosis, andtreatment of infectious disease. ASM supports the clinical microbiological community in manyunique ways – with cutting-edge information, professional certifi cation and awards, and a robust advocacy for the field. Here is how we can help you…

Access to cutting-edge information through:• ASM’s Microbe 2017 meeting, combining the dedicated clinical track of the former General Meeting with the premier infectious disease offerings of ICAAC• ASM Journals – seven journals devoted to clinical microbiology and immunology that delivers authoritative and high-quality clinical research• CUMITECH lab references – now free with membership!• Clinical Microbiology Portal – access to a database of over 1,500 expertly answered questions, and more• Two vibrant listservs dedicated to current clinical issues• NEW MEMBER TYPE: CLS/MT/MLT Labtech Membership with up to 12 CE credits

Certify your accomplishment and expertise through:• Certifi cation by the American Board of Medical Microbiology (ABMM), the American Board of Medical Laboratory Immunology (ABMLI), and the National Registry of Certifi ed Microbiologists (NRCM) • ASM’s Continuing Education (CE) Portal – the online source for accessing and tracking all continuing education activities• Awards and recognition specifi cally focused on clinical microbiologists including the BD Award for Research in Clinical Microbiology, Scherago-Rubin Award, and the Beckman-Coulter Young Investigator Award

Advocacy for the interests of the clinical community through:• Encouraging the adoption of sound policies• Monitoring federal legislation and regulation• Communicating microbiological issues to the public• Participating in CDC/APHL organized meetings

On behalf of the U.S. scientific, engineering, and higher education community we are looking forward to working with you, as 45th President of the United States, and your administration.

As President you will face a wide range of domestic and international challenges, from protecting national and energy security, to ensuring U.S. economic competitiveness, curing diseases, and responding to natural disasters. These challenges share one thing in common: the need for scientific knowledge and technological expertise to address them successfully.

For this reason, we urge that you quickly appoint a science advisor with the title of Assistant to the President for Science and Technology who is a nationally respected leader with the appropriate engineering, scientific, management and policy skills necessary for this critically important role. This senior level advisor can assist you in determining effective ways to use science and technology to address major national challenges. Moreover, this individual can coordinate relevant science and technology policy and personnel decisions within the executive branch of government.

The economic benefits of advancements in science, technology and innovation have been well documented, estimated by leading economists to have accounted for approximately half of U.S. economic growth over the last fifty years. Past government investments in the U.S. scientific and technological enterprise have fueled our economy, created new jobs, and ensured our global competitiveness and national security. At the same time, these investments have enabled the development of a system of U.S. research universities and national laboratories unmatched in the world.

We know that one of your top priorities will be to focus on ensuring that the U.S. economy remains strong and continues to grow. If we are to maintain America’s global leadership, and respond to the economic and security challenges currently facing the nation, we must build on our strong history of federal support for innovation, entrepreneurship and science and technology.

Toward that end we would appreciate the opportunity to meet with you or leaders of your transition team to discuss how the science and engineering community can assist with developing a path forward to ensure that the U.S. innovation infrastructure grows and flourishes under your administration and to suggest candidates for top science and technology posts.

Thank you for your consideration and we look forward to your response. You may contact Joanne Carney (jcarney@aaas.org) with the American Association for the Advancement of Science (AAAS) to coordinate a convenient meeting time, and we will follow up with a proposed list of attendees.

Rush D. Holt
Chief Executive Officer
American Association for the Advancement of Science

The American Society for Microbiology (ASM), headquartered in Washington, DC, is seeking a full-time Volunteer and Governance Engagement Program Coordinator in the Office of the Executive Director department. The incumbent will be responsible for volunteer leadership and governance support, organizational governance nomination, appointments, and recruitment activities and coordinating the annual election of volunteer leadership positions for the Office of the Executive Director. In addition, the incumbent will be responsible for preparing and tracking budget for the volunteer leadership and governance activities.

For a limited time, the first 400 members who renew at the Premium member rate will be given one free membership* to award to the student, postdoc, or colleague of their choice. Hurry and renew! The offer is only good for the first 400 members who renew, and all must be received by October 15, 2016.

HOW IT WORKS:

1) You renew your membership at the Premium level before 10/15/16.

2) Within 2 business days of processing your renewal you will receive an email with an application attached.

3) You select your recipient and forward the application for them to complete and return to ASM. Please note: all awarded membership applications must be received by November 15, 2016.

THE RULES:

-*Only Student, Postdoc, or Supporting memberships are included in this offer.- Recipients cannot have been a member during 2016.- The offer is first-come, first-served: when 400 applications have been awarded the offer will conclude.- Each Premium member is eligible to receive only one free membership.- The free membership cannot be used in combination with any other ASM product to receive a discount, or as part of a Lab & Classroom group.- If are a 2016 Contributing Member and would like to upgrade to Premium in order to take advantage of this offer, either change your member type on the renewal form, and enter $132 for payment OR select Premium membership when renewing online at www.asmscience.org/renew.

For a successful grant application, the typical time from submission to funding is:

a. 1-2 months b. 3-4 months c. 5-6 months d. 7-8 monthse. 9-10 months

The typical length of the grant writing process, from when you begin planning your application to when you receive the funds, is 9-10 months. Since the grant process takes a significant amount of time and has important future implications, it is important to utilize all available resources. One such resource is the ASM Grant Writing Online Course. This three month, six-part webinar series provides graduate, postdoctoral sciences and early to mid-career scientists with an overview of the NIH and NSF grant process. Led by individuals who have successfully obtained grants, this course will provide participants with a broad understanding of (i) the grant making enterprise and the overall funding landscape, (ii) tips for successfully writing NIH and NSF grants, (iii) developing an impactful NIH/NSF Biosketch, and (iv) viewing your grant from the reviewer's perspective.

AUTHORS

Fischer, M. G. | Hackl, T. |

ABSTRACT

Endogenous viral elements are increasingly found in eukaryotic genomes, yet little is known about their origins, dynamics, or function. Here, we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defense system. We found that the virophage mavirus, a parasite of the giant virus CroV, integrates at multiple sites within the nuclear genome of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. The endogenous mavirus is structurally and genetically similar to the eukaryotic Maverick/Polinton DNA transposons. Provirophage genes are activated by superinfection with CroV, which leads to the production of infectious mavirus particles. While provirophage-carrying cells are not directly protected from lysis by CroV, release of reactivated virophage particles promotes survival of other host populations. Our results corroborate the connection between mavirus and Maverick/Polinton elements and suggest that provirophages can defend natural protist populations against infection by giant viruses.

AUTHORS

ABSTRACT

Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

AUTHORS

ABSTRACT

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.

Related Articles

AUTHORS

Haddox, H. K. | Dingens, A. S. | Bloom, J. |

ABSTRACT

HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV's most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV's growth in cell culture. We compare our experimental measurements of each site's preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. We show that some regions of Env have a high inherent tolerance to mutation, whereas other regions (such as epitopes of broadly neutralizing antibodies) have a significantly reduced capacity to tolerate mutations. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env's evolution.

AUTHORS

ABSTRACT

Biofilm formation is a universal bacterial strategy for long-term survival in nature and during infections. Biofilms are dense microbial communities enmeshed within a polymeric extracellular matrix that protects bacteria from antibiotic exposure and the immune system and thus contribute to chronic infections. Pseudomonas aeruginosa is an archetypal biofilm-forming organism that utilizes a biofilm growth strategy to cause chronic lung infections in Cystic Fibrosis (CF) patients. The extracellular matrix of P. aeruginosa biofilms is comprised mainly of exopolysaccharides (EPS) and DNA. Both mucoid and non-mucoid isolates of P. aeruginosa produces the Pel and Psl EPS, each of which have important roles in antibiotic resistance, biofilm formation and immune evasion. Given the central importance of the Pel and Psl EPS in biofilm structure, they are attractive targets for novel anti-infective compounds. In this study we used a high throughput gene expression screen to identify compounds that repress expression of pel and psl genes as measured by transcriptional lux fusions. Testing of the pel/psl repressors demonstrated an antibiofilm activity against microplate and flow chamber biofilms formed by wild type and hyperbiofilm forming strains. To determine the potential role of EPS in virulence, mutants in pel/psl were shown to have reduced virulence in the feeding behavior and slow killing virulence assays in Caenorhabditis elegans. The antibiofilm molecules also reduced P. aeruginosa PAO1 virulence in the nematode slow killing model. Importantly, the combination of antibiotics and antibiofilm compounds were synergistic in killing P. aeruginosa biofilms. These small molecules represent a novel anti-infective strategy for the possible treatment of chronic P. aeruginosa infections.

Related Articles

AUTHORS

Vega, N. | Gore, J. |

ABSTRACT

Host-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here we demonstrate that stochastic bacterial community assembly in the C. elegans intestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

AUTHORS

ABSTRACT

The importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand diet-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-diabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g {beta}-glucan on their habitual diet for 30 days. Fecal bacterial communities in an age-matched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to cereal-bar supplementation are cohort specific and this should be considered when manipulating the microbiome via diet supplementation.

AUTHORS

ABSTRACT

Vibrio cholerae, the causative agent of cholera, is an abundant environmental bacterium that can efficiently colonize the intestinal tract and trigger severe diarrheal illness. Motility, and the production of colonization factors and cholera toxin, are fundamental for the establishment of disease. In the aquatic environment, V. cholerae persists by forming avirulent biofilms on zooplankton, phytoplankton and chitin debris. Here, we describe the formation of artificial, biofilm-like communities, driven by exposure of planktonic bacteria to synthetic polymers. This recruitment is extremely rapid and charge-driven, and leads to the formation of initial 'seed clusters' which then recruit additional bacteria to extend in size. Bacteria that become entrapped in these 'forced communities' undergo transcriptional changes in motility and virulence genes, and phenotypically mimic features of environmental biofilm communities by forming a matrix that contains polysaccharide and extracellular DNA. As a result of this lifestyle transition, pathogenicity and in vivo host colonization decrease. These findings highlight the potential of synthetic polymers to disarm pathogens by modulating their lifestlye, without creating selective pressure favoring the emergence of antimicrobial resistant strains.

AUTHORS

Basharat, Z. | Yasmin, A. |

ABSTRACT

Ruminiclostridium thermocellum strain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach of in silico analysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study.

AUTHORS

ABSTRACT

The genus Streptococcus is one of the most genomically diverse and important human and agricultural pathogens. The acquisition of genomic islands (GIs) plays a central role in adaptation to new hosts in the genus pathogens. The research presented here employs a comparative genomics approach to define a novel family of GIs in the genus Streptococcus which also appears across strains of the same species. Specifically, we identified 9 Streptococcus genomes out of 67 sequenced genomes analyzed, and we termed these as 15bp Streptococcus genomic islands, or 15SGIs, including i) insertion adjacent to the 3' end of ribosome l7/l12 gene, ii) large inserts of horizontally acquired DNA, and iii) the presence of mobility genes (integrase) and replication initiators. We have identified a novel family of 15SGIs and seems to be important in species differentiation and adaptation to new hosts. It plays an important role during strain evolution in the genus Streptococcus.

Related Articles

AUTHORS

Fernandez-Gonzalez, N. | Huber, J. A. | Vallino, J. J. |

ABSTRACT

Although microbial systems are well-suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20 day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function was used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appear inherently well-adapted to disturbances in energy input and that changes in community structure in both treatments are more dependent on internal dynamics than on external forcing. Results also show that the rare biosphere is critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, endogenous feedbacks were more important than exogenous drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and only experience succession or replacement when subject to external perturbations, such as changes in food availability or introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.

AUTHORS

ABSTRACT

The lentivirus equine infectious anemia virus (EIAV) encodes S2, a pathogenic determinant important for virus replication and disease progression in horses. No molecular function has yet been linked to this accessory protein. We now report that S2 can replace the activity of Nef on HIV-1 infectivity, being required to antagonize the inhibitory activity of SERINC proteins on Nef-defective HIV-1. Similar to Nef, S2 excludes SERINC5 from virus particles and requires an ExxxLL motif predicted to recruit the clathrin adaptor AP2. Accordingly, a functional endocytic machinery is essential for S2-mediated infectivity enhancement, which is impaired by inhibitors of clathrin-mediated endocytosis. In addition to retargeting SERINC5 to a late endosomal compartment, S2 promotes the host factor degradation. Emphasizing the similarity with Nef, we show that S2 is myristoylated and, compatible with a crucial role of the post-translational modification, its N-terminal glycine is required for the anti-SERINC5 activity. EIAV-derived vectors devoid of S2 are less susceptible than HIV-1 to the inhibitory effect of both human and equine SERINC5. We then identified the envelope glycoprotein of EIAV as a determinant which also modulates retrovirus susceptibility to SERINC5, indicating a bi-modular ability of the equine lentivirus to counteract the host factor. S2 shares no sequence homology with other retroviral factors known to counteract SERINC5. Adding to primate lentivirus Nef and gammaretrovirus glycoGag, the accessory protein from EIAV makes another example of a retroviral virulence determinant which independently evolved SERINC5-antagonizing activity. SERINC5 therefore plays a critical role for the interaction of the host with diverse retrovirus pathogens.

ABSTRACT

The well-documented significance of microorganisms to the function of virtually all ecosystems has led to the assumption that more information on microbiomes will improve our ability to understand and predict system-level processes. Notably, the importance of the microbiome has become increasingly evident in the environmental sciences and in particular ecosystem ecology. However, translating the ever-increasing wealth of information on environmental microbiomes to advance ecosystem science is proving exceptionally challenging. One reason for this challenge is that correlations between microbiomes and the ecosystem processes they influence are often reported without the underlying causal mechanisms. This limits the predictive power of each correlation to the time and place at which it was identified. In this paper, we assess the assumptions and approaches currently used to establish links between environmental microbiomes and the ecosystems they influence, propose a framework to more effectively harness our understanding of microbiomes to advance ecosystem science, and identify key challenges and solutions required to apply the proposed framework. Specifically, we suggest identifying each microbial process that contributes to the ecosystem process of interest a priori. We then suggest linking information on microbial community membership through microbial community properties (such as biomass elemental ratios) to the microbial processes that drive each ecosystem process (e.g. N -mineralization). A key challenge in this framework will be identifying which microbial community properties can be determined from the constituents of the community (community aggregated traits, CATs) and which properties are unable to be predicted from a list of their constituent taxa (emergent properties, EPs). We view this directed approach as a promising pathway to advance our understanding of how microbiomes influence the systems they inhabit.

AUTHORS

ABSTRACT

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare a total of eight DNA extraction procedures for three specimen types (human feces, pig feces, hospital sewage), assess DNA extraction using spike-in controls and different types of beads for bead-beating facilitating cell lysis. We evaluate DNA concentration, purity, and stability, and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead-beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate compared to standard protocols. Based on this insight, we have designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens.

AUTHORS

Khambhala, P. | Paliwal, P. | Kothari, V. |

ABSTRACT

Microwave mutagenesis of Brevibacillus parabrevis for enhanced cellulase production was attempted. Though microwave treatment could alter the cellulase activity of the test bacterium, none of the mutants obtained were found to be genetically stable, indicating the reversible nature of microwave-induced mutation(s). Thermal stability of the B. parabrevis cellulase was also investigated. This enzyme was found to be capable of retaining its activity even after heat treatment (50-121{degrees}C, for 30-60 min). Fluorescence spectrum revealed a red shift in the emission maxima of the heat-treated enzyme preparations, indicating some structural change upon heating, but no major loss of activity was observed. This enzyme was found to be active over a broad temp range, with 90{degrees}C as the optimum temp, which is interesting as the producing organism is a mesophile.

AUTHORS

Gordon, E. R. L. | McFrederick, Q. S. | Weirauch, C. |

ABSTRACT

The ancient insect order Hemiptera, one of the most well-studied insect lineages with respect to bacterial symbioses, still contains major branches which lack robust phylogenies and comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species]; Pyrrhocoridae [~300 species]) is a superfamily of the primarily-herbivorous hemipteran infraorder Pentatomomorpha, though relationships to related superfamilies are controversial. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes between these putative sister families. We surveyed bacterial diversity of this group using paired-end Illumina and targeted Sanger sequencing of bacterial 16S amplicons of 30 pyrrhocoroid taxa, including 17 species of Largidae, in order to determine the identity of bacterial associates and similarity of associated microbial communities among species. We also constructed the first comprehensive phylogeny of this superfamily (4,800 bp; 5 loci; 57 ingroup + 12 outgroup taxa) in order accurately trace the evolution of symbiotic complexes among Pentatomomorpha. We undertook multiple lines of investigation (i.e., experimental rearing, FISH microscopy, phylogenetic and co-evolutionary analyses) to understand potential transmission routes of largid symbionts. We found a prevalent, specific association of Largidae with plant-beneficial-environmental clade Burkholderia housed in midgut tubules. As in other distantly-related Heteroptera, symbiotic bacteria seem to be acquired from the environment every generation. We review current understanding of symbiotic complexes within the Pentatomomorpha and discuss means to further investigations of the evolution and function of these symbioses. Importance. Obligate symbioses with bacteria are common in insects, particularly for Hemiptera wherein varied forms of symbiosis occur, though knowledge of symbionts remains incomplete for major lineages. Thus, an accurate understanding of how these partnerships evolved and changed over millions of years is not yet achievable. We contribute to our understanding of the evolution of symbiotic complexes in Hemiptera by characterizing bacterial associates of Pyrrhocoroidea focusing on the family Largidae and by constructing a phylogeny to establish evolutionary relationships of and within this group. Members of Largidae are associated with specific symbiotic Burkholderia from a different clade than Burkholderia symbionts in other Hemiptera and are members of the earliest-diverging superfamily of Burkholderia-associated Hemiptera. Evidence suggests that species of Largidae reacquire specific symbiotic bacteria every generation environmentally, a rare strategy for insects with potentially volatile evolutionary ramifications, but one that has persisted in Largidae and other related lineages since the Cretaceous.

AUTHORS

ABSTRACT

Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 - 2015. Preliminary data indicated the involvement of two distinct yet related bacterial populations, one from San Diego and San Joaquin (SD/SJ) and one from the San Francisco (SF) Bay area. Whole genome sequencing of sixty-eight outbreak and archival isolates of S. sonnei was performed to investigate the microbiological factors related to these outbreaks. Both SD/SJ and SF populations, as well as almost all of the archival S. sonnei isolates belonged to sequence type 152 (ST152). Genome-wide SNP analysis clustered the majority of California (CA) isolates to an earlier described global Lineage III, which has persisted in CA since 1986. Isolates in the SD/SJ population had a novel Shiga-toxin (STX)-encoding lambdoid bacteriophage, most closely related to that found in an Escherichia coli O104:H4 strain responsible for a large outbreak. However, the STX genes (stx1a and stx1b) from this novel phage had sequences most similar to the phages from S. flexneri and S. dysenteriae. The isolates in the SF population yielded evidence of fluoroquinolone resistance acquired via the accumulation of point mutations in gyrA and parC genes. Thus, the CA S. sonnei lineage continues to evolve by the acquisition of increased virulence and antibiotic resistance, and enhanced monitoring is advocated for its early detection in future outbreaks.

Related Articles

AUTHORS

Preisner, E. C. | Fichot, E. B. | Norman, R. S. |

ABSTRACT

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the activity of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. While this ecosystem undergoes a range of seasonal variation, it experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and activity of abundant and rare taxa, suggesting overall functional and compositional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low activity across conditions, the total number of active taxa and overall activity increased post-disturbance, with significant shifts in activity occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and activity. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.

ABSTRACT

Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted laboratory evolution by daily dilution in increasing concentrations of benzoic acid (from 5 to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from the evolving populations showed change in phenotype from benzoate-sensitive to benzoate-tolerant but sensitive to chloramphenicol and tetracycline. Sixteen clones isolated at 2,000 generations grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth profiles were seen in 10 mM salicylate. The strains showed growth profiles indistinguishable from W3110 in the absence of benzoate; in media buffered at pH 4.8, pH 7.0, or pH 9.0; or in 20 mM acetate or sorbate at pH 6.5. The genomes of 16 strains revealed over 100 mutations including SNPs, large deletions, and insertion sequence knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or associated regulators such as rob and cpx, as well as MDR efflux pumps emrA, emrY, and mdtA. Strains also lost or down-regulated the Gad acid fitness regulon. In 5 mM benzoate, or in 2 mM salicylate, most strains showed increased sensitivity to the antibiotic chloramphenicol, some more sensitive than a marA knockout. Thus, the benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance.

AUTHORS

ABSTRACT

Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Koch's postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

Related Articles

AUTHORS

Harrison, F. | Diggle, S. P. |

ABSTRACT

A key aim in microbiology is to determine the genetic and phenotypic bases of bacterial virulence, persistence and antimicrobial resistance in chronic biofilm infections. This requires tractable, high-throughput models that reflect the physical and chemical environment encountered in specific infection contexts. Such models will increase the predictive power of microbiological experiments and provide platforms for enhanced testing of novel antibacterial or antivirulence therapies. We present an optimised ex vivo model of cystic fibrosis lung infection: ex vivo culture of pig bronchiolar tissue in artificial cystic fibrosis mucus. We focus on the formation of biofilms by Pseudomonas aeruginosa. We show highly repeatable and specific formation of biofilms that resemble clinical biofilms by a commonly-studied lab strain and ten cystic fibrosis isolates of this key opportunistic pathogen.

AUTHORS

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Some microbes can transition from an environmental lifestyle to a pathogenic one. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes. However, the genomic features that must be present in a population prior to the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, using Vibrio cholerae as a model. We then characterized several environmental VAP alleles to show that one of them reduced the ability of clinical strains to colonize a mammalian host, whereas two other alleles conferred efficient colonization. These results show that VAPs are present in environmental bacterial populations prior to the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment, they become selected and enriched under certain ecological conditions, and finally a genomic background containing several VAPs acquires virulence factors that allows for its emergence as a pathogenic clone.

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Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial taxa to capture electrons from a cathode and fix carbon. Yet the metabolic capacity of multispecies microbial communities on electrosynthetic biocathodes remains unknown. We assembled 13 genomes from a high-performing electroacetogenic culture, and mapped their transcriptional activity from a range of conditions. This allowed us to create a metabolic model of the primary community members (Acetobacterium, Sulfurospirillum, and Desulfovibrio). Acetobacterium was the primary carbon fixer, and a keystone member of the community. Based on transcripts upregulated near the electrode surface, soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were essential conduits for electron flow from the electrode into the electrosynthetic community. A nitrogenase gene cluster with an adjacent ferredoxin and one of two Rnf complexes within the genome of the Acetobacterium were also upregulated on the electrode. Nitrogenase is known to serve as a hydrogenase, thereby it would contribute to hydrogen production by the biocathode. Oxygenases of microaerobic members of the community throughout the cathode chamber, including Sulfurospirillum and Rhodobacteraceae, were expressed. While the reactors were maintained anaerobically, this gene expression would support anaerobic growth and thus electrosynthesis by scrubbing small amounts of O2 out of the reactor. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.

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Biofuel alcohols have severe consequences on the microbial hosts used in their biosynthesis, which limits the productivity of the bioconversion. The cell envelope is one of the most strongly affected structures, in particular, as the external concentration of biofuels rises during biosynthesis. Damage to the cell envelope can have severe consequences, such as impairment of transport into and out of the cell; however the nature of butanol-induced envelope damage has not been well characterized. In the present study, the effects of n-butanol on the cell envelope of Escherichia coli were investigated. Using enzyme and fluorescence-based assays, we observed that 1% v/v n-butanol resulted in release of lipopolysaccharides from the outer membrane of E. coli and caused leakiness in both outer and inner membranes. Higher concentrations of n-butanol, within the range of 2% - 10% (v/v), resulted in inner membrane protrusion through the peptidoglycan observed by characteristic blebs. The findings suggest that strategies for rational engineering of butanol-tolerant bacterial strains should take into account all components of the cell envelope.

ABSTRACT

Zika virus (ZIKV) is a member of Flaviviridae family, as other agents of clinical significance, such as dengue (DENV) and hepatitis C (HCV) viruses. ZIKV spread from Africa to Pacific and South American territories, emerging as an etiological pathogen of neurological disorders, during fetal development and in adulthood. Therefore, antiviral drugs able to inhibit ZIKV replication are necessary. Broad spectrum antivirals, such as interferon, ribavirin and favipiravir, are harmful for pregnant animal models and women. The clinically approved uridine nucleotide analog anti-HCV drug, sofosbuvir, has not been affiliated to teratogenicity. Sofosbuvir target the most conserved protein over the members of the Flaviviridae family, the viral RNA polymerase. We thus studied ZIKV susceptibility to sofosbovir. We initially characterized a Brazilian ZIKV strain for use in experimental assays. Sofosbuvir inhibits the Brazilian ZIKV replication in a dose-dependent manner, both in BHK-21 cells and SH-Sy5y, by targeting ZIKV RNA polymerase activity, with the involvement of conserved amino acid residues over the members of Flaviviridae family. The identification of clinically approved antiviral drugs endowed with anti-ZIKV could reduce the time frame in pre-clinical development. Altogether, our data indicates that sofosbuvir chemical structure is endowed with anti-ZIKV activity.

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Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from antibiotic efficacy studies, studies of growth under different nutritional or stress environments, to studies of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.

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Zika Virus (ZIKV) is a causative agent for poor pregnancy outcome and fetal developmental abnormalities, including microcephaly and eye defects. As a result, ZIKV is now a confirmed teratogen. Understanding host-pathogen interactions, specifically cellular perturbations caused by ZIKV, can provide novel therapeutic targets. In order to complete viral replication, viral pathogens control the host cellular machineries and regulate various factors, including long non-coding RNA (lncRNA) genes, at transcriptional levels. The role of lncRNA genes in the pathogenesis of ZIKV-mediated microcephaly and eye defects is currently unknown. To gain additional insights, we focused on profiling the differentially expressed lncRNA genes during ZIKV infection in mammalian cells. For this study, we employed a contemporary clinical Zika viral isolate, PRVABC59, of Asian genotype. We utilized an unbiased RNA sequencing approach to profile the lncRNA transcriptome in ZIKV infected Vero cells. We identified a total of 121 lncRNA genes that are differentially regulated at 48 hours post-infection. The majority of these genes are independently validated by reverse-transcription qPCR. A notable observation was that the lncRNAs, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and NEAT1 (Nuclear Paraspeckle Assembly Transcript 1), are down-regulated upon Zika viral infection. MALAT1 and NEAT1 are known as nuclear localized RNAs that regulate gene expression and cell proliferation. Protein-lncRNA interaction maps revealed that MALAT1 and NEAT1 share common interacting partners and form a larger network comprising of 71 cellular factors. ZIKV-mediated dysregulation of these two regulatory lncRNAs can alter the expression of respective target genes and associated biological functions, an important one being cell division. In conclusion, this investigation is the first to provide insight into the biological connection of lncRNAs and ZIKV which can be further explored for developing antiviral therapy and understanding fetal developmental processes.

Related Articles

AUTHORS

Granato, E. T. | Harrison, F. | Kummerli, R. | Ross-Gillespie, A. |

ABSTRACT

Bacterial traits that contribute to disease are termed 'virulence factors' and there is much interest in therapeutic approaches that disrupt such traits. However, ecological theory predicts disease severity to be multifactorial and context dependent, which might complicate our efforts to identify the most generally important virulence factors. Here, we use meta-analysis to quantify disease outcomes associated with one well-studied virulence factor - pyoverdine, an iron-scavenging compound secreted by the opportunistic pathogen Pseudomonas aeruginosa. Consistent with ecological theory, we found that the effect of pyoverdine, albeit frequently contributing to disease, varied considerably across infection models. In many cases its effect was relatively minor, suggesting that pyoverdine is rarely essential for infections. Our work demonstrates the utility of meta-analysis as a tool to quantify variation and overall effects of purported virulence factors across different infection models. This standardised approach will help us to evaluate promising targets for anti-virulence approaches.

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Mukherjee, N. | Sulaiman, I. M. | Banerjee, P. |

ABSTRACT

Indoor skin-contact surfaces of public fitness centers may serve as reservoirs of potential human transmission of methicillin-resistant Staphylococcus aureus (MRSA). We found a high prevalence of multi-drug resistant (MDR)-MRSA of CC59 lineage harboring a variety of extracellular toxin genes from surface swab samples collected from inanimate surfaces of fitness centers in Memphis metropolitan area, USA. Our findings underscore the role of inanimate surfaces as potential sources of transmission of MDR-MRSA strains with considerable genetic diversity.

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ABSTRACT

Noroviruses produce viral RNAs lacking a 5' cap structure and instead use a virus-encoded VPg protein covalently linked to viral RNA to interact with translation initiation factors and drive viral protein synthesis. Norovirus infection results in the induction of the innate response leading to interferon stimulated gene (ISG) transcription. However the translation of the induced ISG mRNAs is suppressed. Using a novel mass spectrometry approach we demonstrate that diminished host mRNA translation correlates with changes to the composition of the eukaryotic initiation factor complex. The suppression of host ISG translation correlates with the activity of the viral protease (NS6) and the activation of cellular caspases leading to the establishment of an apoptotic environment. These results indicate that noroviruses exploit the differences between viral VPg-dependent and cellular cap-dependent translation in order to diminish the host response to infection.

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While it is generally thought that bacteria are bad for us, research has shown that bacteria are important in our health and possibly longevity. Bacteria inhabit just about every part of the human body ranging from the skin, nose and the intestinal tract. In fact, bacteria make up more cells in the body than human cells and are collectively known as the microbiome. The microbiome of the intestine has been shown to play a role in disease such as obesity and diabetes. The intestinal microbiota has also been linked to a variety of beneficial functions that include the breakdown of nutrients, vitamin production and development of the immune system. For over 50 years, research has shown that reducing the amount of food an animal consumes (a process known as calorie restriction, CR) increases lifespan by retarding aging because most age-related diseases are delayed or reduced by CR. Because diet and age can exert major effects on the composition of the intestinal microbiota, we hypothesized that CR, specifically 40% restriction, would delay/prevent age related changes in the intestinal microbiota.

Researchers from the University of Oklahoma Health Sciences Center (OUHSC) and the Missouri Mutant Mouse Resource and Research Center (MU MMRRC) studied the effect of age and life-long CR on the composition of the intestinal microbiota of young and old laboratory mice. The results will be presented at the ASM Microbe in Boston, Massachusetts on Saturday June 18, 2016.

As mice age, significant changes in the composition of the microbiota were observed. For example, there was a decrease or absence of specific bacteria in the old mice that were present in the young mice. Conversely, there were also bacteria that were found in the old mice but not in the young mice. In addition to the changes described above, overall, there was about a 30% reduction in the number of different types of bacteria found in the old mice compared to the young mice.

CR altered the overall composition of the intestinal microbiota of old mice in comparison to their old counterparts that were given unlimited access to food. The old calorie restricted mice contained a microbiome profile that was highly similar to that found in the young mice. Additionally, with the old calorie restricted mice there were no age-related reductions in the number of different types of bacteria and were comparable to that of the young mice.

From this study, researchers were able to demonstrate for the first time that CR prevented the age-related changes in the intestinal microbiome. The implications of this data suggests that the preservation of the young intestinal microbiota profile found within old CR mice may play a role in the prevention or delay of age-related diseases as well as the extension in lifespan seen with CR. Additional research will be needed to determine if these differences in the microbiome are beneficial or harmful as well as determine whether or not these changes play a role in the extension of lifespan.

This study will be presented on at the American Society for Microbiology’s Microbe 2016 meeting in Boston, MA.

Ongoing Monitoring of Legionella in Flint in the Wake of the Drinking Water CrisisDr. Otto Schwake

Eight strains of Legionella isolated from a health care center in Flint, MI during March 2016. Photograph: Otto Schwake

Samples of discolored tap water and a rusty water filter provided by Flint residents. Photograph: Virgina Tech/Jim Stroup

Sharing of Tooth Decay Causing Bacterium Among Children and Their FamiliesStephanie Momeni

S. mutans colony morphology

Research Shows New Mechanism That Can Cause Eye InflammationDr. Robert Shanks

Pseudo-colored electron micrograph of Serratia marcescens bacteria (red) on a human corneal cell in vitro. The yellow arrow indicates a large surface bleb induced by a toxin produced by the bacteria. The white bar indicates 10 microns.

A Novel Therapy for Genital Herpes Engages Immune Cells to Provide Significant Patient Benefits for at Least a YearDr. Kenneth Fife, MD, PhD, investigator and Professor of Medicine at Indiana University

Fig. 1: sMFC components and experimental installation plan depict two sMFCs with identical sediment-buried graphite anodes wired (in red) to transmit microbially-generated electric current from anodes to an upper cellular data relay unit (upper box) that transmits the data from the field site. Electrons then pass via wires (green) to carbon cloth cathodes (grey ovals) suspended in the water at variable depths. Leftmost sMFC features a surface cathode while the sMFC at right has a submerged cathode. Identical replicate sMFCs (not shown) were included in the study.